Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems

(2019) M. E. Sieracki et al.   Scientific Reports

The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments

(2019) Susanne Wilken et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

(2018) Yoann Seeleuthner et al.   Nature Communications

Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

(2018) Guy Leonard et al.   Open Biology

Deep mitochondrial origin outside the sampled alphaproteobacteria

(2018) Joran Martijn et al.   NATURE

Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates

(2017) Jürgen F H Strassert et al.   ISME Journal

Morphological Identification and Single-Cell Genomics of Marine Diplonemids

(2016) Ryan M.R. Gawryluk et al.   CURRENT BIOLOGY

Genomics: Evolution of the Genetic Code

(2016) Patrick J. Keeling   CURRENT BIOLOGY

A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae

(2016) Tereza Ševčíková et al.   Genome Biology and Evolution

Mitochondrial Genome ofPalpitomonas bilix: Derived Genome Structure and Ancestral System for CytochromecMaturation

(2016) Yuki Nishimura et al.   Genome Biology and Evolution

A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts)

(2016) Romain Derelle et al.   MOLECULAR BIOLOGY AND EVOLUTION

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention

(2016) Iain G. Johnston et al.   Cell Systems

Complete mitochondrial genome of a DHA-rich protist Schizochytrium sp. TIO1101

(2016) Zhaokai Wang et al.   Mitochondrial DNA Part B-Resources

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data

(2015) Konstantin Okonechnikov et al.   BIOINFORMATICS

Divergent Mitochondrial Respiratory Chains in Phototrophic Relatives of Apicomplexan Parasites

(2015) Pavel Flegontov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes

(2015) A. Z. Worden et al.   SCIENCE

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes

(2014) Sivakumar Kannan et al.   BMC EVOLUTIONARY BIOLOGY

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles

(2013) Ramon Massana et al.   ISME Journal

Horizontal gene transfer in osmotrophs: playing with public goods

(2013) Thomas A. Richards et al.   NATURE REVIEWS MICROBIOLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Global distribution of a wild alga revealed by targeted metagenomics

(2012) Alexandra Z. Worden et al.   CURRENT BIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis

(2012) Debashish Bhattacharya et al.   Scientific Reports

Marine Fungi: Their Ecology and Molecular Diversity

(2011) Thomas A. Richards et al.   Annual Review of Marine Science

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

Unveiling in situ interactions between marine protists and bacteria through single cell sequencing

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus

(2011) Elif Demir-Hilton et al.   ISME Journal

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

(2010) M. L. Cuvelier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Seven Gene Phylogeny of Heterokonts

(2009) Ingvild Riisberg et al.   PROTIST

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

The CGView Server: a comparative genomics tool for circular genomes

(2008) J. R. Grant et al.   NUCLEIC ACIDS RESEARCH